One Step Closer to Personal Antimicrobial Treatment

Harmless intestinal bacteria may transfer resistance genes to pathogenic bacteria, making the dangerous bacteria resistant to antimicrobial agents. A new method makes it possible to locate resistance genes quickly and thus choose the most effective type of treatment with antimicrobial agents.

Taking antibiotics against an infection will not necessarily solve your problems. The fact is that the naturally occurring intestinal bacteria often possess resistance genes.

This means that the intestinal bacteria may exchange genes with the pathogenic bacteria, making the dangerous bacteria resistant to treatment with antimicrobial agents. It is therefore crucial to know the resistome—i.e. the pool of resistance genes present in the intestine. This enables doctors to choose the most effective treatment.

Researchers from the Novo Nordisk Foundation Center for Biosustainability—DTU Biosustain—at DTU have developed an ultrafast, inexpensive method called poreFUME, which may shed light on intestinal resistance genes.

“This method gives you an overview of the resistome in just 1-2 days, enabling quicker treatment of the infection and improved results,” says Eric van der Helm, Postdoc at DTU Biosustain.
The research results were recently published in the journal Nucleic Acid Research.

Antimicrobial resistance causes 700,000 deaths a year

The poreFUME method is very fast compared with the current methods, because it does not require cultivation of faecal bacteria. Cultivation takes time and can also be difficult.

“We are absolutely convinced that quick resistome analysis may lead to personal antimicrobial treatment in high-risk patients.”

Morten Sommer, Professor at DTU Biosustain

An analysis of the resistome currently takes weeks. In the meantime, the resistome profile may change dramatically, resulting in deterioration of the infection and failure of the patient’s health.

700,000 people die of resistant infections each year, especially hospitalized patients—and the problem is growing. For many patients, a quick analysis of their personal resistance genes in their faeces may be life-saving.

“Our research shows that this method is a promising alternative to other sequencing methods, and that it can be used to provide a quick profile of the resistome in the microbial communities in, for example, the intestines. We are absolutely convinced that quick resistome analysis may lead to personal antimicrobial treatment in high-risk patients,” says Morten Sommer, co-author of the article and Professor at DTU Biosustain.

Inexpensive tests make the difference

The study was conducted as a joint project between DTU and Dr Willem van Schaik from University Medical Center Utrecht, who had access to a patient from the intensive care unit. In the study, five faecal samples from the patient were examined.

The patient had COPD and underwent a lung transplantation, after which the doctors provided treatment with four different kinds of antimicrobial agents to prevent and fight infections. The faecal samples were collected on admission to the intensive care unit, during the patient’s stay and several months after the admission.

The results showed that the poreFUME method was 97 per cent accurate compared with standardized methods, which is sufficient.

In addition, the poreFUME method is much more inexpensive than the current methods, mainly because of the low price of the so-called MinION machine; a small hand-held DNA sequencing unit, which costs about USD 1,000. In comparison, conventional so-called next-generation sequencing machines often cost from around USD 50,000 to USD 10 million.

“If hospitals can buy resistome analysis equipment at a lower price than today, this will pave the way for better profiling of more patients and hopefully fewer cases of resistance,” says Lejla Imamovic, co-author of the article and researcher at DTU Biosustain.

Nanopores register every DNA building block

The MinION DNA sequencing machine can detect electrical impulses from DNA building blocks

The first step in finding the resistome is to isolate all the DNA from the microbes that are involved in the development of resistance. The DNA is broken down into two strands, and a single strand is passed down through the MinION sequencing machine, which contains so-called nanopores.

Each nanopore is only a couple of nano-metres wide and can only contain one DNA strand at a time.

The nanopore then measures the electrical impulses from the different DNA building blocks, which are placed inside the pore.